In some cases, it may be technically illegal, but if nobody knows about it, it doesn't matter. In most cases, the guys who make the rules also make the laws, so it's not illegal. It's simply the way the business gets done. It's called "maintaining an orderly market." If you don't like it, every time you buy a stock, have it "registered and shipped." Then place the certificate in a safe place. It will cost you extra, but it's the only way you can know that people aren't playing around with your stock while you're not looking, loaning it to each other, making their books look bigger, borrowing against it, etc.
With KATX, you could take your certs and use them as toilet paper.